megadetector 5.0.28__py3-none-any.whl → 5.0.29__py3-none-any.whl

megadetector/data_management/importers/save_the_elephants_survey_B.py

@@ -1,329 +0,0 @@
-"""
-
- save_the_elephants_survey_B.py
-
- Convert the .csv file provided for the Save the Elephants Survey B data set to a 
- COCO-camera-traps .json file
-
-"""
-
-#%% Constants and environment
-
-import pandas as pd
-import os
-import json
-import uuid
-import time
-import humanfriendly
-import numpy as np
-from tqdm import tqdm
-
-from megadetector.utils.path_utils import find_images
-from megadetector.visualization import visualize_db
-from megadetector.data_management.databases import integrity_check_json_db
-
-input_base = r'z:/ste_2019_08_drop'
-# input_base = r'/mnt/blobfuse/wildlifeblobssc/ste_2019_08_drop'
-input_metadata_file = os.path.join(input_base,'SURVEY B.xlsx')
-
-output_base = r'f:/save_the_elephants/survey_b'
-# output_base = r'/home/gramener/survey_b'
-output_json_file = os.path.join(output_base,'ste_survey_b.json')
-image_directory = os.path.join(input_base,'SURVEY B with False Triggers')
-                        
-os.makedirs(output_base,exist_ok=True)
-assert(os.path.isdir(image_directory))
-assert(os.path.isfile(input_metadata_file))
-
-# Handle all unstructured fields in the source data as extra fields in the annotations
-mapped_fields = {'No. of Animals in Photo':'num_animals',
-                 'No. of new indiviauls (first sighting of new individual)':'num_new_individuals',
-                 'Number Adult Males (first sighting of new individual)':'num_adult_males',
-                 'Number Adult Females (first sighting of new individual)':'num_adult_females',
-                 'Number Adult Unknown (first sighting of new individual)':'num_adult_unknown',
-                 'Number Sub-adult Males (first sighting of new individual)':'num_subadult_males',
-                 'Number Sub-adult Females (first sighting of new individual)':'num_subadult_females',
-                 'Number Sub-adult Unknown (first sighting of new individual)':'num_subadult_unknown',
-                 'Number Juvenile (first sighting of new individual)':'num_juvenile',
-                 'Number Newborn (first sighting of new individual)':'num_newborn',
-                 'Activity':'activity',
-                 'Animal ID':'animal_id',
-                 'Specific Notes':'notes'}
-
-# photo_type really should be an image property, but there are a few conflicts
-# that forced me to handle it as an annotation proprerty
-mapped_fields['Photo Type '] = 'photo_type'
-
-#%% Read source data
-
-input_metadata = pd.read_excel(input_metadata_file, sheet_name='9. CT Image')
-input_metadata = input_metadata.iloc[2:]
-
-print('Read {} columns and {} rows from metadata file'.format(len(input_metadata.columns),
-      len(input_metadata)))
-
-
-#%% Map filenames to rows, verify image existence
-
-#%% Map filenames to rows, verify image existence
-
-start_time = time.time()
-
-# Maps relative paths to row indices in input_metadata
-filenames_to_rows = {}
-filenames_with_multiple_annotations = []
-missing_images = []
-
-# Build up a map from filenames to a list of rows, checking image existence as we go
-for i_row, fn in tqdm(enumerate(input_metadata['Image Name']), total=len(input_metadata)):
-    try:
-        # Ignore directories
-        if not fn.endswith('.JPG'):
-            continue
-
-        if fn in filenames_to_rows:
-            filenames_with_multiple_annotations.append(fn)
-            filenames_to_rows[fn].append(i_row)
-        else:
-            filenames_to_rows[fn] = [i_row]
-            image_path = os.path.join(image_directory, fn)
-            if not os.path.isfile(image_path):
-                missing_images.append(image_path)
-    except:
-        continue
-
-elapsed = time.time() - start_time
-
-print('Finished verifying image existence for {} files in {}, found {} filenames with multiple labels, {} missing images'.format(
-      len(filenames_to_rows), humanfriendly.format_timespan(elapsed),
-      len(filenames_with_multiple_annotations), len(missing_images)))
-
-#%% Make sure the multiple-annotation cases make sense
-
-if False:
-
-    #%%
-
-    fn = filenames_with_multiple_annotations[1000]
-    rows = filenames_to_rows[fn]
-    assert(len(rows) > 1)
-    for i_row in rows:
-        print(input_metadata.iloc[i_row]['Species'])
-
-#%% Check for images that aren't included in the metadata file
-
-# Enumerate all images
-image_full_paths = find_images(image_directory, bRecursive=True)
-
-unannotated_images = []
-
-for iImage, image_path in tqdm(enumerate(image_full_paths),total=len(image_full_paths)):
-    relative_path = os.path.relpath(image_path,image_directory)
-    if relative_path not in filenames_to_rows:
-        unannotated_images.append(relative_path)
-
-print('Finished checking {} images to make sure they\'re in the metadata, found {} unannotated images'.format(
-        len(image_full_paths),len(unannotated_images)))
-
-
-#%% Create CCT dictionaries
-
-images = []
-annotations = []
-categories = []
-
-image_ids_to_images = {}
-
-category_name_to_category = {}
-
-# Force the empty category to be ID 0
-empty_category = {}
-empty_category['name'] = 'empty'
-empty_category['id'] = 0
-category_name_to_category['empty'] = empty_category
-categories.append(empty_category)
-next_category_id = 1
-
-start_time = time.time()
-# i_image = 0; image_name = list(filenames_to_rows.keys())[i_image]
-for image_name in tqdm(list(filenames_to_rows.keys())):
-
-    # Example filename:
-    #        
-    # 'Site 1_Oloisukut_1\Oloisukut_A11_UP\Service_2\100EK113\EK001382.JPG'
-    # 'Site 1_Oloisukut_1\Oloisukut_A11_UP\Service_2.1\100EK113\EK001382.JPG'
-    img_id = image_name.replace('\\','/').replace('\n','').replace('/','_').replace(' ','_')
-    
-    row_indices = filenames_to_rows[image_name]
-    
-    # i_row = row_indices[0]
-    for i_row in row_indices:
-        
-        row = input_metadata.iloc[i_row]
-        assert(row['Image Name'] == image_name)
-        try:
-            timestamp = row['Date'].strftime("%d/%m/%Y")
-        except:
-            timestamp = ""
-        # timestamp = row['Date']
-        station_label = row['Camera Trap Station Label']
-        photo_type = row['Photo Type ']
-        if isinstance(photo_type,float):
-            photo_type = ''
-        photo_type = photo_type.strip().lower()
-            
-        if img_id in image_ids_to_images:
-            
-            im = image_ids_to_images[img_id]
-            assert im['file_name'] == image_name
-            assert im['station_label'] == station_label
-            
-            # There are a small handful of datetime mismatches across annotations
-            # for the same image
-            # assert im['datetime'] == timestamp
-            if im['datetime'] != timestamp:
-                print('Warning: timestamp conflict for image {}: {},{}'.format(
-                    image_name,im['datetime'],timestamp))
-                
-        else:
-            
-            im = {}
-            im['id'] = img_id
-            im['file_name'] = image_name
-            im['datetime'] = timestamp
-            im['station_label'] = station_label
-            im['photo_type'] = photo_type
-            
-            image_ids_to_images[img_id] = im
-            images.append(im)
-    
-        species = row['Species']
-        
-        if (isinstance(species,float) or \
-            (isinstance(species,str) and (len(species) == 0))):
-            category_name = 'empty'
-        elif species.startswith('?'):
-            category_name = 'unknown'
-        else:
-            category_name = species
-        
-        # Special cases based on the 'photo type' field
-        if 'vehicle' in photo_type:
-            category_name = 'vehicle'
-        # Various spellings of 'community'
-        elif 'comm' in photo_type:
-            category_name = 'human'
-        elif 'camera' in photo_type or 'researcher' in photo_type:
-            category_name = 'human'
-        elif 'livestock' in photo_type:
-            category_name = 'livestock'
-        elif 'blank' in photo_type:
-            category_name = 'empty'
-        elif 'plant movement' in photo_type:
-            category_name = 'empty'
-            
-        category_name = category_name.strip().lower()
-            
-        # Have we seen this category before?
-        if category_name in category_name_to_category:
-            category_id = category_name_to_category[category_name]['id'] 
-        else:
-            category_id = next_category_id
-            category = {}
-            category['id'] = category_id
-            category['name'] = category_name
-            category_name_to_category[category_name] = category
-            categories.append(category)
-            next_category_id += 1
-        
-        # Create an annotation
-        ann = {}        
-        ann['id'] = str(uuid.uuid1())
-        ann['image_id'] = im['id']    
-        ann['category_id'] = category_id
-        
-        # fieldname = list(mapped_fields.keys())[0]
-        for fieldname in mapped_fields:
-            target_field = mapped_fields[fieldname]
-            val = row[fieldname]
-            if isinstance(val,float) and np.isnan(val):
-                val = ''
-            else:
-                val = str(val).strip()
-            ann[target_field] = val
-            
-        annotations.append(ann)
-        
-    # ...for each row
-                
-# ...for each image
-    
-print('Finished creating CCT dictionaries in {}'.format(
-      humanfriendly.format_timespan(elapsed)))
-    
-
-#%% Create info struct
-
-info = {}
-info['year'] = 2019
-info['version'] = 1
-info['description'] = 'Save the Elephants Survey B'
-info['contributor'] = 'Save the Elephants'
-
-
-#%% Write output
-
-json_data = {}
-json_data['images'] = images
-json_data['annotations'] = annotations
-json_data['categories'] = categories
-json_data['info'] = info
-json.dump(json_data, open(output_json_file, 'w'), indent=2)
-
-print('Finished writing .json file with {} images, {} annotations, and {} categories'.format(
-        len(images),len(annotations),len(categories)))
-
-
-#%% Validate output
-
-from megadetector.data_management.databases import integrity_check_json_db
-
-options = integrity_check_json_db.IntegrityCheckOptions()
-options.baseDir = image_directory
-options.bCheckImageSizes = False
-options.bCheckImageExistence = False
-options.bFindUnusedImages = False
-    
-sortedCategories, data = integrity_check_json_db.integrity_check_json_db(output_json_file,options)
-
-
-#%% Preview labels
-
-from megadetector.visualization import visualize_db
-from megadetector.data_management.databases import integrity_check_json_db
-
-viz_options = visualize_db.DbVizOptions()
-viz_options.num_to_visualize = 1000
-viz_options.trim_to_images_with_bboxes = False
-viz_options.add_search_links = True
-viz_options.sort_by_filename = False
-viz_options.parallelize_rendering = True
-html_output_file,image_db = visualize_db.visualize_db(db_path=output_json_file,
-                                                        output_dir=os.path.join(output_base,'preview'),
-                                                        image_base_dir=image_directory,
-                                                        options=viz_options)
-os.startfile(html_output_file)
-
-
-#%% Scrap
-
-if False:
-
-    pass
-    
-    #%% Find unique photo types
-    
-    annotations = image_db['annotations']
-    photo_types = set()
-    for ann in tqdm(annotations):
-        photo_types.add(ann['photo_type'])